[English] 日本語
Yorodumi- PDB-5mnc: Cationic trypsin in complex with aniline (deuterated sample at 100 K) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mnc | ||||||
---|---|---|---|---|---|---|---|
Title | Cationic trypsin in complex with aniline (deuterated sample at 100 K) | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE / hydrogen bonding / protonation / protein-ligand interaction | ||||||
Function / homology | Function and homology information cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.916 Å | ||||||
Authors | Schiebel, J. / Heine, A. / Klebe, G. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Charges Shift Protonation: Neutron Diffraction Reveals that Aniline and 2-Aminopyridine Become Protonated Upon Binding to Trypsin. Authors: Schiebel, J. / Gaspari, R. / Sandner, A. / Ngo, K. / Gerber, H.D. / Cavalli, A. / Ostermann, A. / Heine, A. / Klebe, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5mnc.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5mnc.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mnc_validation.pdf.gz | 441 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5mnc_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 5mnc_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 5mnc_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/5mnc ftp://data.pdbj.org/pub/pdb/validation_reports/mn/5mnc | HTTPS FTP |
-Related structure data
Related structure data | 5mn1C 5mnaC 5mnbC 5mnxC 5mnyC 5monC 5mooC 4i8hS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ANL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 15% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.7069 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7069 Å / Relative weight: 1 |
Reflection | Resolution: 0.916→42.245 Å / Num. obs: 146365 / % possible obs: 97.9 % / Redundancy: 6.507 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 18.82 |
Reflection shell | Resolution: 0.916→0.97 Å / Redundancy: 6.13 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.74 / % possible all: 94.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I8H Resolution: 0.916→14.291 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 9.85
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.916→14.291 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|